Iodine in PDB 1lkr: Monoclinic Hen Egg White Lysozyme Iodide
Enzymatic activity of Monoclinic Hen Egg White Lysozyme Iodide
All present enzymatic activity of Monoclinic Hen Egg White Lysozyme Iodide:
3.2.1.17;
Protein crystallography data
The structure of Monoclinic Hen Egg White Lysozyme Iodide, PDB code: 1lkr
was solved by
L.K.Steinrauf,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
1.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
27.894,
63.153,
60.227,
90.00,
90.12,
90.00
|
R / Rfree (%)
|
14 /
14
|
Iodine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
17;
Binding sites:
The binding sites of Iodine atom in the Monoclinic Hen Egg White Lysozyme Iodide
(pdb code 1lkr). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 17 binding sites of Iodine where determined in the
Monoclinic Hen Egg White Lysozyme Iodide, PDB code: 1lkr:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iodine binding site 1 out
of 17 in 1lkr
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Iodine Binding Sites List in 1lkr
Iodine binding site 1 out
of 17 in the Monoclinic Hen Egg White Lysozyme Iodide
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Monoclinic Hen Egg White Lysozyme Iodide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I130
b:3.4
occ:0.63
|
CA
|
A:ARG21
|
3.9
|
3.0
|
1.0
|
C
|
A:ARG21
|
3.9
|
2.8
|
1.0
|
N
|
A:GLY22
|
4.1
|
2.5
|
1.0
|
O
|
A:HOH152
|
4.1
|
0.9
|
1.0
|
N
|
A:ARG21
|
4.5
|
1.8
|
1.0
|
O
|
A:ARG21
|
4.5
|
3.0
|
1.0
|
CD
|
A:ARG21
|
4.8
|
8.5
|
0.6
|
CA
|
A:GLY22
|
4.9
|
2.2
|
1.0
|
|
Iodine binding site 2 out
of 17 in 1lkr
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Iodine Binding Sites List in 1lkr
Iodine binding site 2 out
of 17 in the Monoclinic Hen Egg White Lysozyme Iodide
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Monoclinic Hen Egg White Lysozyme Iodide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I132
b:6.2
occ:0.52
|
CD
|
A:ARG5
|
3.9
|
2.4
|
1.0
|
NZ
|
A:LYS33
|
3.9
|
7.5
|
1.0
|
NE
|
A:ARG5
|
4.0
|
2.1
|
1.0
|
O
|
A:HOH309
|
4.2
|
8.1
|
0.5
|
CE2
|
A:PHE38
|
4.2
|
3.7
|
1.0
|
CZ3
|
A:TRP123
|
4.4
|
9.9
|
1.0
|
CB
|
A:ARG5
|
4.4
|
2.2
|
1.0
|
O
|
A:HOH415
|
4.5
|
5.5
|
0.5
|
CE
|
A:LYS33
|
4.6
|
0.1
|
1.0
|
CD
|
A:LYS33
|
4.6
|
7.0
|
1.0
|
CG
|
A:ARG5
|
4.7
|
2.6
|
1.0
|
CZ
|
A:PHE38
|
4.8
|
2.6
|
1.0
|
O
|
A:HOH326
|
5.0
|
4.5
|
0.5
|
|
Iodine binding site 3 out
of 17 in 1lkr
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Iodine Binding Sites List in 1lkr
Iodine binding site 3 out
of 17 in the Monoclinic Hen Egg White Lysozyme Iodide
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Monoclinic Hen Egg White Lysozyme Iodide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I133
b:1.9
occ:0.34
|
OD1
|
A:ASP87
|
3.2
|
3.8
|
0.5
|
N
|
A:ILE88
|
3.5
|
4.7
|
1.0
|
CG1
|
A:ILE88
|
3.7
|
4.8
|
1.0
|
CA
|
A:ASP87
|
3.8
|
7.8
|
1.0
|
O
|
A:HOH165
|
3.9
|
3.8
|
0.5
|
O
|
A:HOH232
|
4.0
|
1.1
|
0.5
|
CG
|
A:ASP87
|
4.1
|
2.1
|
0.7
|
NH2
|
A:ARG14
|
4.1
|
3.6
|
1.0
|
C
|
A:ASP87
|
4.2
|
6.7
|
1.0
|
CB
|
A:ALA11
|
4.2
|
1.9
|
1.0
|
CE1
|
A:HIS15
|
4.2
|
0.5
|
1.0
|
CB
|
A:ILE88
|
4.5
|
5.3
|
1.0
|
CA
|
A:ILE88
|
4.6
|
4.3
|
1.0
|
CZ
|
A:PHE3
|
4.6
|
4.2
|
1.0
|
CG2
|
A:ILE88
|
4.7
|
6.9
|
1.0
|
CD1
|
A:ILE88
|
4.8
|
7.2
|
1.0
|
O
|
A:SER86
|
4.8
|
9.7
|
1.0
|
OD2
|
A:ASP87
|
4.9
|
6.0
|
0.5
|
CB
|
A:ASP87
|
5.0
|
9.5
|
1.0
|
|
Iodine binding site 4 out
of 17 in 1lkr
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Iodine Binding Sites List in 1lkr
Iodine binding site 4 out
of 17 in the Monoclinic Hen Egg White Lysozyme Iodide
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Monoclinic Hen Egg White Lysozyme Iodide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I134
b:6.1
occ:0.27
|
O
|
B:HOH198
|
2.8
|
5.1
|
1.0
|
O
|
A:ASN106
|
3.6
|
7.1
|
1.0
|
O
|
A:HOH457
|
3.8
|
3.2
|
0.5
|
O
|
A:HOH430
|
3.9
|
3.6
|
0.5
|
C
|
A:ASN106
|
3.9
|
2.5
|
1.0
|
CB
|
A:ASN103
|
4.1
|
2.6
|
1.0
|
CG
|
A:ASN103
|
4.1
|
5.4
|
1.0
|
N
|
A:ALA107
|
4.1
|
3.0
|
1.0
|
CA
|
A:ALA107
|
4.2
|
3.1
|
1.0
|
CB
|
A:ASN106
|
4.3
|
3.3
|
1.0
|
ND2
|
A:ASN103
|
4.4
|
2.0
|
1.0
|
OD1
|
A:ASN103
|
4.4
|
9.8
|
1.0
|
O
|
A:HOH350
|
4.4
|
3.6
|
0.5
|
O
|
A:HOH180
|
4.7
|
3.1
|
1.0
|
CA
|
A:ASN106
|
4.7
|
1.1
|
1.0
|
O
|
B:HOH330
|
4.9
|
4.9
|
0.5
|
|
Iodine binding site 5 out
of 17 in 1lkr
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Iodine Binding Sites List in 1lkr
Iodine binding site 5 out
of 17 in the Monoclinic Hen Egg White Lysozyme Iodide
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Monoclinic Hen Egg White Lysozyme Iodide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I135
b:1.0
occ:0.58
|
O
|
A:HOH199
|
3.5
|
2.6
|
1.0
|
O
|
A:HOH189
|
3.6
|
6.3
|
1.0
|
ND2
|
A:ASN113
|
3.8
|
2.1
|
0.8
|
CB
|
A:ASN113
|
4.1
|
5.7
|
1.0
|
CA
|
A:ALA110
|
4.2
|
1.7
|
1.0
|
CG
|
A:ASN113
|
4.4
|
8.2
|
0.9
|
O
|
A:HOH276
|
4.4
|
6.1
|
0.5
|
CB
|
A:ALA110
|
4.4
|
4.0
|
1.0
|
CD
|
A:ARG114
|
4.5
|
9.0
|
1.0
|
CG
|
A:ARG114
|
4.6
|
7.4
|
1.0
|
O
|
A:VAL109
|
4.8
|
0.7
|
1.0
|
N
|
A:ALA110
|
4.8
|
1.6
|
1.0
|
|
Iodine binding site 6 out
of 17 in 1lkr
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Iodine Binding Sites List in 1lkr
Iodine binding site 6 out
of 17 in the Monoclinic Hen Egg White Lysozyme Iodide
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Monoclinic Hen Egg White Lysozyme Iodide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I140
b:9.2
occ:0.25
|
OH
|
A:TYR23
|
3.4
|
5.9
|
1.0
|
O
|
A:HOH175
|
3.5
|
5.7
|
1.0
|
CE
|
A:LYS116
|
3.9
|
4.3
|
1.0
|
OD1
|
B:ASN77
|
3.9
|
9.9
|
0.7
|
ND2
|
A:ASN106
|
4.0
|
8.2
|
1.0
|
CH2
|
A:TRP111
|
4.2
|
0.5
|
1.0
|
CZ
|
A:TYR23
|
4.3
|
3.1
|
1.0
|
O
|
A:HOH304
|
4.3
|
2.8
|
0.5
|
CE1
|
A:TYR23
|
4.3
|
2.1
|
1.0
|
NZ
|
A:LYS116
|
4.4
|
6.9
|
1.0
|
CZ3
|
A:TRP111
|
4.8
|
0.4
|
1.0
|
CG
|
A:ASN106
|
4.8
|
3.7
|
1.0
|
OD1
|
A:ASN106
|
4.8
|
5.7
|
1.0
|
CG
|
B:ASN77
|
4.9
|
5.7
|
0.7
|
|
Iodine binding site 7 out
of 17 in 1lkr
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Iodine Binding Sites List in 1lkr
Iodine binding site 7 out
of 17 in the Monoclinic Hen Egg White Lysozyme Iodide
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Monoclinic Hen Egg White Lysozyme Iodide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I141
b:9.5
occ:0.23
|
O
|
A:HOH155
|
3.8
|
6.8
|
0.5
|
CA
|
A:ARG14
|
4.0
|
4.9
|
1.0
|
CG
|
A:LYS13
|
4.1
|
5.0
|
0.8
|
O
|
A:LYS13
|
4.1
|
2.3
|
1.0
|
N
|
A:ARG14
|
4.3
|
2.8
|
1.0
|
CE
|
A:LYS13
|
4.4
|
4.8
|
0.6
|
NZ
|
A:LYS13
|
4.4
|
4.6
|
0.3
|
C
|
A:LYS13
|
4.4
|
2.4
|
1.0
|
O
|
A:HOH301
|
4.4
|
1.6
|
0.5
|
CD
|
A:LYS13
|
4.7
|
4.6
|
0.8
|
CB
|
A:LYS13
|
4.7
|
3.6
|
1.0
|
CB
|
A:ARG14
|
4.8
|
7.1
|
0.8
|
|
Iodine binding site 8 out
of 17 in 1lkr
Go back to
Iodine Binding Sites List in 1lkr
Iodine binding site 8 out
of 17 in the Monoclinic Hen Egg White Lysozyme Iodide
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 8 of Monoclinic Hen Egg White Lysozyme Iodide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I142
b:4.0
occ:0.23
|
CG
|
A:GLN121
|
2.7
|
0.3
|
0.6
|
NE2
|
A:GLN121
|
2.8
|
1.2
|
0.3
|
O
|
A:HOH392
|
3.3
|
7.6
|
0.5
|
OG
|
A:SER24
|
3.3
|
5.7
|
1.0
|
CD
|
A:GLN121
|
3.4
|
0.5
|
0.5
|
N
|
A:GLY26
|
3.4
|
8.4
|
1.0
|
CB
|
A:SER24
|
3.7
|
3.0
|
1.0
|
CA
|
A:GLN121
|
3.8
|
8.5
|
1.0
|
CB
|
A:GLN121
|
3.9
|
9.4
|
1.0
|
CD1
|
A:ILE124
|
3.9
|
6.9
|
1.0
|
CA
|
A:GLY26
|
3.9
|
9.1
|
1.0
|
N
|
A:LEU25
|
4.2
|
0.1
|
1.0
|
N
|
A:GLN121
|
4.3
|
6.8
|
1.0
|
C
|
A:SER24
|
4.4
|
0.8
|
1.0
|
CG1
|
A:ILE124
|
4.5
|
1.8
|
1.0
|
C
|
A:LEU25
|
4.6
|
9.5
|
1.0
|
CA
|
A:LEU25
|
4.6
|
9.1
|
1.0
|
O
|
A:VAL120
|
4.7
|
8.8
|
1.0
|
CA
|
A:SER24
|
4.7
|
1.6
|
1.0
|
C
|
A:VAL120
|
4.7
|
5.5
|
1.0
|
C
|
A:GLN121
|
4.7
|
7.5
|
1.0
|
CB
|
A:LEU25
|
4.8
|
9.6
|
1.0
|
OE1
|
A:GLN121
|
4.9
|
0.8
|
0.2
|
C
|
A:GLY26
|
5.0
|
8.3
|
1.0
|
|
Iodine binding site 9 out
of 17 in 1lkr
Go back to
Iodine Binding Sites List in 1lkr
Iodine binding site 9 out
of 17 in the Monoclinic Hen Egg White Lysozyme Iodide
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 9 of Monoclinic Hen Egg White Lysozyme Iodide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I143
b:6.3
occ:0.24
|
CD
|
A:ARG45
|
3.7
|
2.0
|
0.2
|
O
|
A:HOH431
|
4.0
|
3.4
|
0.5
|
NE
|
A:ARG45
|
4.1
|
2.5
|
0.5
|
O
|
A:HOH328
|
4.9
|
1.0
|
0.5
|
O
|
A:HOH418
|
5.0
|
1.9
|
0.5
|
|
Iodine binding site 10 out
of 17 in 1lkr
Go back to
Iodine Binding Sites List in 1lkr
Iodine binding site 10 out
of 17 in the Monoclinic Hen Egg White Lysozyme Iodide
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 10 of Monoclinic Hen Egg White Lysozyme Iodide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I144
b:5.5
occ:0.68
|
ND2
|
A:ASN74
|
3.8
|
2.9
|
1.0
|
N
|
A:PRO79
|
4.0
|
2.8
|
1.0
|
CD
|
A:PRO79
|
4.1
|
3.6
|
1.0
|
C
|
A:ILE78
|
4.1
|
4.5
|
1.0
|
ND2
|
A:ASN65
|
4.3
|
9.6
|
1.0
|
CA
|
A:ILE78
|
4.3
|
7.1
|
1.0
|
O
|
A:ILE78
|
4.4
|
3.6
|
1.0
|
CB
|
A:ASN65
|
4.5
|
8.6
|
1.0
|
N
|
A:ILE78
|
4.5
|
6.4
|
1.0
|
CA
|
A:PRO79
|
4.5
|
1.9
|
1.0
|
C
|
A:ASN77
|
4.6
|
8.3
|
1.0
|
CB
|
A:PRO79
|
4.7
|
2.7
|
1.0
|
O
|
A:ASN77
|
4.8
|
9.2
|
1.0
|
CG
|
A:ASN74
|
4.8
|
9.6
|
1.0
|
CG
|
A:PRO79
|
4.9
|
3.6
|
1.0
|
ND2
|
A:ASN77
|
4.9
|
2.4
|
0.7
|
|
Reference:
L.K.Steinrauf,
L.K.Steinrauf.
N/A N/A.
ISSN: ISSN 0907-4449
PubMed: 9757091
DOI: 10.1107/S0907444997016922
Page generated: Sun Aug 11 12:28:04 2024
|